On the fourth page of this article is a sentence – “Hence, we replaced the HMR-E variant (AAACCCATAAC) with the genome-wide consensus sequence for the Rap1 protein (ACACCCATACATT).” This sentence is three years of my life.

This is a story about an article roughly four years in the making; about my fascination with how a tiny animal moves; and about the experimentation that was necessary before I could answer the questions that first piqued my interest.

The problem of biases in small RNA deep-sequencing is so interesting and important that journals will let researchers repeatedly publish the same results and conclusions provided they claim originality and cite the literature.

...I needed to pause my main project and quickly publish a paper on the artifact, to alert the community. I presented this to a number of labs and the contradictory advice that I got from brilliant researchers made me dizzy.

...A paper on which I am the senior author is being published in Nature... Today in this blog I am going to do my best to tell the story behind the paper - about the people and the process and a little bit about the science.

Well, I have truly entered the modern world. My first PLoS One paper has just come out. It is entitled "An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)" and well, it describes automated software for analyzing rRNA sequences that are generated as part of microbial diversity studies. The main goal behind this was to keep up with the massive amounts of rRNA sequences we and others could generate in the lab and to develop a tool that would remove the need for "manual" work in analyzing rRNAs.

...Publishing this paper with PeerJ has been a fun ride, both because the staff have been so responsive and the platform is so well-designed, but also because we have had a chance to test-drive new features as they are introduced. Our unreviewed manuscript was the first PeerJ PrePrint, and now that it has been published, we have already started interacting with readers via PeerJ’s innovative new Q&A feature.

...research suggested that the tiny single-celled parasite had evolved a way to specifically alter the innate hard-wired aversion that rodents had to cats for its own benefit. I honestly couldn’t believe it. While the studies seemed to be designed well and the results looked pretty solid, there were a lot of questions left unanswered. My curiosity got the best of me and I designed a thesis project to answer the question, ‘If this parasite causes loss of aversion to cats in mice, what is the mechanism by which it accomplishes this?

...Doing the sampling was time-consuming and demanding in the extreme, but I was so eager to know what was happening that I spent Christmas Day of 2010 collecting samples, the ones that ultimate were used for our article. It is still the longest, the happiest and the most exciting Christmas Day I have had in my life.

… I was determined to learn something about the regulation of meiotic double-strand break formation by studying DSB-1. Even after my thesis committee suggested that maybe I should consider pursuing another project, I still couldn’t give it up. DSB-1 was, after all, my scientific baby.

This paper is about how mucins, a family of glycoproteins that composes our mucus, can be used as a cell-repellent coating for cell patterning. But this is also a story about how perseverance, good communication and a bit of luck are key in research.

Way back when I was just a fledgling graduate student, even before the NYT bestseller The Immortal Life of Henrietta Lacks by Rebecca Skloot, I proposed to my PI the idea of sequencing the genome of HeLa cells. At the time all I knew was that they were ubiquitous, fast growing and robust enough that a post doc in my undergraduate lab taught cell culture techniques to me with them, stating “don’t worry – you can’t screw up with HeLa”. Years later I can say with confidence that I am no longer that fled

My PI, Mike Eisen, is famous for his outspoken views on Open Access—including his willingness to put his money where his mouth is: he co-founded PLoS and the lab only publishes in OA journals. In addition to believing that the current system doesn't let enough people read the literature, Mike has long felt that the rate of science publishing is too slow, meaning that interesting results don't appear in print until months, or sometimes years, after the work has been done.

One aspect of working in molecular biology is that all discoveries in the end are probably inevitable. Someone will figure it out eventually. There are too many smart or lucky people thinking lots of different ways for this not to be the case.

It was a really cool moment, because it was one of those rare instances when you have an idea and you just know it will work deep down in your gut. It was also a really special moment for me as a PI, because it was Marshall's idea, and I was so very proud of him for coming up with it.

I chatted with my new PI about potential research projects
and chose what I thought was a novel and innovative project. At the
same time, I was training to run a marathon. I probably should have
realized what to expect over the next three years when he told me,
“Training for this marathon is going to be so easy compared to the
project you’ve undertaken.”

As scientists, most of us are focused on carrying out experiments and
gathering data – but working on this manuscript really showed all of
us just how important it is to spend just as much time on thinking
about exactly how to depict all this data.

This finding started with the collision of a physicist and a biologist
in the corridors of the École Normale Supérieure. While this event
looked random at the time, I feel now that the weight of several
generations of our peers had a lot to do with placing us in those
corridors and creating the necessary conditions for the fruitful
result of those seemingly random collisions.

Here I am baring my soul, so be sure to keep this to yourself and your
closest friends. I have a remarkable lack of interest in anything I
did in the past, and reserve most of my passion and interest for what
is going on now or will be going on in the future. Hence, once the
work was done and the mutants sent to anyone who wanted them, I just
lacked the juice to get the damn thing written.

Some [papers] are simply the result of hard work, persistence and
follow-through and as such, eventually fade into the background. But
others become so intertwined with the entirety of your life that they
become fixed points in your timeline.